BACKGROUND: There is paucity of information about Anaplasma marginale (A. marginale) infection in water buffaloes and there have not been any reports of clinical anaplasmosis in the buffaloes in Iran. OBJECTIVES: Molecular and hematologic survey on A. marginale infection in apparently healthy buffaloes referring to Ahvaz abattoir. METHODS: Samples of blood and spleen tissue were obtained from 103 healthy buffaloes referring to the slaughterhouse. Blood samples were subjected to microscopic examination and PCR assay while spleen specimens were only analyzed by PCR. In this study, a nested-PCR method was used to amplify a fragment of the groEL gene of the bacterium. RESULTS: According to PCR, 31.1% and 1.9% of examined blood and spleen samples were found positive for A. marginale, respectively. The buffaloes which were positive in spleen tissue PCR test were positive in blood PCR, as well. Microscopically, Anaplasma-like organisms were found in 15.5% of stained blood smears. There was a slight Kappa agreement between stained blood smears and PCR. No significant difference was found in hematologic values between the infected and non-infected buffaloes based on PCR results. CONCLUSIONS: Significant occurrence of infection with A. marginale in the studied buffaloes can indicate the probable role of buffalo as a reservoir of the disease agent and its transmission to the cattle.